OMG, that's it... I ran into the same with Easy Nivo Slider plugin activated on the first site in my network blocking access to the Network Admin section. And indeed it has a file called settings.php. And a similar thing happens when there is a file called options.php: the Site Admin section is no longer accessible.
Disabling the plugin solved the issue. Then after renaming the file settings.php to(for example) settings-form.php and editing the include statement to keep funcitonality of the plugin itself, I could run both the plugin and access Network Admin at the same time.
To replicate the issue:
- Do a clean WP install and upgrade to Multi Site;
- install Easy Nivo Slider or any other plugin that has a file called settings.php or options.php in it;
- enable it on the main site;
- try to access the Network Admin section...
- rename the plugins file settings.php or options.php to anything else
- adapt the include statement in the main plugin file to reflect the new name
When a plugin file bears the name settings.php, Network Admin is blocked. When a plugin includes a plugin file called options.php, the Site Admin is blocked.
It looks to me like this is a WordPress bug. I've only tested this on a 3.2.1 multi-site install that has been recently upgraded from 3.0 so no idea if this behaviour always occurs but in theory, it should not matter how individual plugin files are named. Or am I mistaken?